diff --git a/examples/benchmark_amg.cpp b/examples/benchmark_amg.cpp
index c79b9e64..885c387c 100644
--- a/examples/benchmark_amg.cpp
+++ b/examples/benchmark_amg.cpp
@@ -10,6 +10,8 @@
 
 #include "raptor/raptor.hpp"
 
+using namespace raptor;
+
 int main(int argc, char* argv[])
 {
     MPI_Init(&argc, &argv);
diff --git a/examples/benchmark_matmult.cpp b/examples/benchmark_matmult.cpp
index 489c7782..618b9458 100644
--- a/examples/benchmark_matmult.cpp
+++ b/examples/benchmark_matmult.cpp
@@ -20,7 +20,7 @@
 #include "external/mfem_wrapper.hpp"
 #endif
 
-// using namespace raptor;
+using namespace raptor;
 int main(int argc, char *argv[])
 {
     MPI_Init(&argc, &argv);
diff --git a/examples/benchmark_matops.cpp b/examples/benchmark_matops.cpp
index 9063e898..8573db8c 100644
--- a/examples/benchmark_matops.cpp
+++ b/examples/benchmark_matops.cpp
@@ -22,6 +22,8 @@
   #include "external/mfem_wrapper.hpp"
 #endif
 
+using namespace raptor;
+
 #define eager_cutoff 1000
 #define short_cutoff 62
 
diff --git a/examples/benchmark_nek5000.cpp b/examples/benchmark_nek5000.cpp
index d3659c17..669d51bd 100644
--- a/examples/benchmark_nek5000.cpp
+++ b/examples/benchmark_nek5000.cpp
@@ -8,9 +8,11 @@
 
 #include "clear_cache.hpp"
 
-#include "core/types.hpp"
-#include "multilevel/par_multilevel.hpp"
-#include "external/hypre_wrapper.hpp"
+#include "raptor/core/types.hpp"
+#include "raptor/multilevel/par_multilevel.hpp"
+#include "raptor/external/hypre_wrapper.hpp"
+
+using namespace raptor;
 
 int main(int argc, char *argv[])
 {
diff --git a/examples/benchmark_par_spmv.cpp b/examples/benchmark_par_spmv.cpp
index a8f7e8c3..73ab0bce 100644
--- a/examples/benchmark_par_spmv.cpp
+++ b/examples/benchmark_par_spmv.cpp
@@ -11,10 +11,10 @@
 #include "raptor/raptor.hpp"
 
 #ifdef USING_MFEM
-#include "external/mfem_wrapper.hpp"
+#include "raptor/external/mfem_wrapper.hpp"
 #endif
 
-//using namespace raptor;
+using namespace raptor;
 int main(int argc, char *argv[])
 {
     MPI_Init(&argc, &argv);
diff --git a/examples/benchmark_pcg.cpp b/examples/benchmark_pcg.cpp
index 5d82377f..b3feafc9 100644
--- a/examples/benchmark_pcg.cpp
+++ b/examples/benchmark_pcg.cpp
@@ -10,6 +10,7 @@
 
 #include "raptor/raptor.hpp"
 
+using namespace raptor;
 int main(int argc, char* argv[])
 {
     MPI_Init(&argc, &argv);
diff --git a/examples/benchmark_reader.cpp b/examples/benchmark_reader.cpp
index b37d998a..7db31c9f 100644
--- a/examples/benchmark_reader.cpp
+++ b/examples/benchmark_reader.cpp
@@ -9,6 +9,7 @@
 
 #include "raptor/raptor.hpp"
 
+using namespace raptor;
 int main(int argc, char* argv[])
 {
     MPI_Init(&argc, &argv);
diff --git a/examples/benchmark_rss.cpp b/examples/benchmark_rss.cpp
index e0cc7e3d..3727055a 100644
--- a/examples/benchmark_rss.cpp
+++ b/examples/benchmark_rss.cpp
@@ -8,23 +8,23 @@
 
 #include "clear_cache.hpp"
 
-#include "core/par_matrix.hpp"
-#include "core/par_vector.hpp"
-#include "core/types.hpp"
-#include "gallery/par_stencil.hpp"
-#include "gallery/laplacian27pt.hpp"
-#include "gallery/diffusion.hpp"
-#include "gallery/par_matrix_IO.hpp"
-#include "ruge_stuben/par_ruge_stuben_solver.hpp"
-#include "external/hypre_wrapper.hpp"
-#include "krylov/par_cg.hpp"
+#include "raptor/core/par_matrix.hpp"
+#include "raptor/core/par_vector.hpp"
+#include "raptor/core/types.hpp"
+#include "raptor/gallery/par_stencil.hpp"
+#include "raptor/gallery/laplacian27pt.hpp"
+#include "raptor/gallery/diffusion.hpp"
+#include "raptor/gallery/par_matrix_IO.hpp"
+#include "raptor/ruge_stuben/par_ruge_stuben_solver.hpp"
+#include "raptor/external/hypre_wrapper.hpp"
+#include "raptor/krylov/par_cg.hpp"
 
 #ifdef USING_MFEM
-  #include "external/mfem_wrapper.hpp"
+  #include "raptorexternal/mfem_wrapper.hpp"
 #endif
 
-//using namespace raptor;
-//
+using namespace raptor;
+
 
 void form_hypre_weights(std::vector<double>& weights, int n_rows)
 {
diff --git a/examples/benchmark_setup.cpp b/examples/benchmark_setup.cpp
index 0404e924..410d6c56 100644
--- a/examples/benchmark_setup.cpp
+++ b/examples/benchmark_setup.cpp
@@ -8,18 +8,19 @@
 
 #include "clear_cache.hpp"
 
-#include "core/par_matrix.hpp"
-#include "core/par_vector.hpp"
-#include "core/types.hpp"
-#include "gallery/par_stencil.hpp"
-#include "gallery/laplacian27pt.hpp"
-#include "gallery/diffusion.hpp"
-#include "gallery/par_matrix_IO.hpp"
-#include "ruge_stuben/par_ruge_stuben_solver.hpp"
+#include "raptor/core/par_matrix.hpp"
+#include "raptor/core/par_vector.hpp"
+#include "raptor/core/types.hpp"
+#include "raptor/gallery/par_stencil.hpp"
+#include "raptor/gallery/laplacian27pt.hpp"
+#include "raptor/gallery/diffusion.hpp"
+#include "raptor/gallery/par_matrix_IO.hpp"
+#include "raptor/ruge_stuben/par_ruge_stuben_solver.hpp"
 
 #define eager_cutoff 8000
 #define short_cutoff 496
 
+using namespace raptor;
 int main(int argc, char *argv[])
 {
 
diff --git a/examples/benchmark_setup_sweeps.cpp b/examples/benchmark_setup_sweeps.cpp
index 85b1e2e1..7ba0ae6f 100644
--- a/examples/benchmark_setup_sweeps.cpp
+++ b/examples/benchmark_setup_sweeps.cpp
@@ -9,6 +9,7 @@
 #include "clear_cache.hpp"
 
 #include "raptor/raptor.hpp"
+using namespace raptor;
 
 int main(int argc, char* argv[])
 {
diff --git a/examples/benchmark_solve.cpp b/examples/benchmark_solve.cpp
index 7e8ce414..6a5b8714 100644
--- a/examples/benchmark_solve.cpp
+++ b/examples/benchmark_solve.cpp
@@ -8,18 +8,20 @@
 
 #include "clear_cache.hpp"
 
-#include "core/par_matrix.hpp"
-#include "core/par_vector.hpp"
-#include "core/types.hpp"
-#include "gallery/par_stencil.hpp"
-#include "gallery/laplacian27pt.hpp"
-#include "gallery/diffusion.hpp"
-#include "gallery/par_matrix_IO.hpp"
-#include "ruge_stuben/par_ruge_stuben_solver.hpp"
+#include "raptor/core/par_matrix.hpp"
+#include "raptor/core/par_vector.hpp"
+#include "raptor/core/types.hpp"
+#include "raptor/gallery/par_stencil.hpp"
+#include "raptor/gallery/laplacian27pt.hpp"
+#include "raptor/gallery/diffusion.hpp"
+#include "raptor/gallery/par_matrix_IO.hpp"
+#include "raptor/ruge_stuben/par_ruge_stuben_solver.hpp"
 
 #define eager_cutoff 8000
 #define short_cutoff 496
 
+using namespace raptor;
+
 int main(int argc, char *argv[])
 {
 
diff --git a/examples/benchmark_spgemm_overlap.cpp b/examples/benchmark_spgemm_overlap.cpp
index 5ca9cdba..374d9aa2 100644
--- a/examples/benchmark_spgemm_overlap.cpp
+++ b/examples/benchmark_spgemm_overlap.cpp
@@ -10,6 +10,8 @@
 
 #include "raptor/raptor.hpp"
 
+using namespace raptor;
+
 int main(int argc, char* argv[])
 {
     MPI_Init(&argc, &argv);
diff --git a/examples/benchmark_spmv.cpp b/examples/benchmark_spmv.cpp
index f8028daa..ae9f40f4 100644
--- a/examples/benchmark_spmv.cpp
+++ b/examples/benchmark_spmv.cpp
@@ -7,15 +7,15 @@
 #include "clear_cache.hpp"
 #include <ctime>
 
-#include "core/matrix.hpp"
-#include "core/vector.hpp"
-#include "core/types.hpp"
-#include "gallery/stencil.hpp"
-#include "gallery/laplacian27pt.hpp"
-#include "gallery/diffusion.hpp"
-#include "gallery/matrix_IO.hpp"
-
-//using namespace raptor;
+#include "raptor/core/matrix.hpp"
+#include "raptor/core/vector.hpp"
+#include "raptor/core/types.hpp"
+#include "raptor/gallery/stencil.hpp"
+#include "raptor/gallery/laplacian27pt.hpp"
+#include "raptor/gallery/diffusion.hpp"
+#include "raptor/gallery/matrix_IO.hpp"
+
+using namespace raptor;
 
 double wtime()
 {
diff --git a/examples/benchmark_spmv_overlap.cpp b/examples/benchmark_spmv_overlap.cpp
index a48efb6b..f96184e2 100644
--- a/examples/benchmark_spmv_overlap.cpp
+++ b/examples/benchmark_spmv_overlap.cpp
@@ -10,6 +10,8 @@
 
 #include "raptor/raptor.hpp"
 
+using namespace raptor;
+
 int main(int argc, char* argv[])
 {
     MPI_Init(&argc, &argv);
diff --git a/examples/benchmark_tap_amg.cpp b/examples/benchmark_tap_amg.cpp
index 32b2ec7e..0efe259c 100644
--- a/examples/benchmark_tap_amg.cpp
+++ b/examples/benchmark_tap_amg.cpp
@@ -10,6 +10,8 @@
 
 #include "raptor/raptor.hpp"
 
+using namespace raptor;
+
 void form_hypre_weights(double** weight_ptr, int n_rows)
 {
     int rank;
diff --git a/examples/benchmark_tap_spgemm.cpp b/examples/benchmark_tap_spgemm.cpp
index cd44bcf6..b9d4bcd6 100644
--- a/examples/benchmark_tap_spgemm.cpp
+++ b/examples/benchmark_tap_spgemm.cpp
@@ -8,23 +8,25 @@
 
 #include "clear_cache.hpp"
 
-#include "core/par_matrix.hpp"
-#include "core/par_vector.hpp"
-#include "core/types.hpp"
-#include "gallery/par_stencil.hpp"
-#include "gallery/laplacian27pt.hpp"
-#include "gallery/diffusion.hpp"
-#include "gallery/par_matrix_IO.hpp"
-#include "multilevel/par_multilevel.hpp"
-#include "ruge_stuben/par_ruge_stuben_solver.hpp"
+#include "raptor/core/par_matrix.hpp"
+#include "raptor/core/par_vector.hpp"
+#include "raptor/core/types.hpp"
+#include "raptor/gallery/par_stencil.hpp"
+#include "raptor/gallery/laplacian27pt.hpp"
+#include "raptor/gallery/diffusion.hpp"
+#include "raptor/gallery/par_matrix_IO.hpp"
+#include "raptor/multilevel/par_multilevel.hpp"
+#include "raptor/ruge_stuben/par_ruge_stuben_solver.hpp"
 
 #ifdef USING_MFEM
-#include "external/mfem_wrapper.hpp"
+#include "raptor/external/mfem_wrapper.hpp"
 #endif
 
 #define eager_cutoff 1000
 #define short_cutoff 62
 
+using namespace raptor;
+
 void print_times(double time, double time_comm, const char* name)
 {
     int rank;
diff --git a/examples/benchmark_tap_spmv.cpp b/examples/benchmark_tap_spmv.cpp
index 442a791f..cfbb08f9 100644
--- a/examples/benchmark_tap_spmv.cpp
+++ b/examples/benchmark_tap_spmv.cpp
@@ -8,24 +8,25 @@
 
 #include "clear_cache.hpp"
 
-#include "core/par_matrix.hpp"
-#include "core/par_vector.hpp"
-#include "core/types.hpp"
-#include "gallery/par_stencil.hpp"
-#include "gallery/laplacian27pt.hpp"
-#include "gallery/diffusion.hpp"
-#include "gallery/par_matrix_IO.hpp"
-#include "multilevel/par_multilevel.hpp"
-#include "ruge_stuben/par_ruge_stuben_solver.hpp"
+#include "raptor/core/par_matrix.hpp"
+#include "raptor/core/par_vector.hpp"
+#include "raptor/core/types.hpp"
+#include "raptor/gallery/par_stencil.hpp"
+#include "raptor/gallery/laplacian27pt.hpp"
+#include "raptor/gallery/diffusion.hpp"
+#include "raptor/gallery/par_matrix_IO.hpp"
+#include "raptor/multilevel/par_multilevel.hpp"
+#include "raptor/ruge_stuben/par_ruge_stuben_solver.hpp"
 
 #ifdef USING_MFEM
-  #include "external/mfem_wrapper.hpp"
+  #include "raptor/external/mfem_wrapper.hpp"
 #endif
 
 
 #define eager_cutoff 1000
 #define short_cutoff 62
 
+using namespace raptor;
 
 int main(int argc, char *argv[])
 {
diff --git a/examples/clear_cache.hpp b/examples/clear_cache.hpp
index 45eaea5b..0812fb4b 100644
--- a/examples/clear_cache.hpp
+++ b/examples/clear_cache.hpp
@@ -7,7 +7,7 @@
 #include <time.h>
 #include <math.h>
 #include <vector>
-#include "core/types.hpp"
+#include "raptor/core/types.hpp"
 
 using namespace raptor;
 
diff --git a/examples/coo_example.cpp b/examples/coo_example.cpp
index 8fc02126..a4712b6b 100644
--- a/examples/coo_example.cpp
+++ b/examples/coo_example.cpp
@@ -9,6 +9,8 @@
 // Include raptor
 #include "raptor/raptor.hpp"
 
+using namespace raptor;
+
 // This example creates a random ParCSRMatrix
 // All values are added into COO format and then converted.
 // The example then performs a SpMV on this matrix
diff --git a/examples/csr_example.cpp b/examples/csr_example.cpp
index 82078779..b653e387 100644
--- a/examples/csr_example.cpp
+++ b/examples/csr_example.cpp
@@ -9,6 +9,7 @@
 // Include raptor
 #include "raptor/raptor.hpp"
 
+using namespace raptor;
 // This example creates a random ParCSRMatrix
 // All values are added directly into ParCSR format.
 // The example then performs a SpMV on this matrix
diff --git a/examples/example.cpp b/examples/example.cpp
index 1e36687a..a901c3aa 100644
--- a/examples/example.cpp
+++ b/examples/example.cpp
@@ -9,6 +9,8 @@
 // Include raptor
 #include "raptor/raptor.hpp"
 
+using namespace raptor;
+
 // This is a basic use case.
 int main(int argc, char *argv[])
 {
diff --git a/examples/matop_example.cpp b/examples/matop_example.cpp
index 7e483c73..ca2d4517 100644
--- a/examples/matop_example.cpp
+++ b/examples/matop_example.cpp
@@ -9,6 +9,8 @@
 // Include raptor
 #include "raptor/raptor.hpp"
 
+using namespace raptor;
+
 // This is a basic use case.
 int main(int argc, char *argv[])
 {
diff --git a/examples/model_tap_steps.cpp b/examples/model_tap_steps.cpp
index 8b9360d3..29142a01 100644
--- a/examples/model_tap_steps.cpp
+++ b/examples/model_tap_steps.cpp
@@ -9,7 +9,7 @@
 #include "clear_cache.hpp"
 
 #include "raptor/raptor.hpp"
-
+using namespace raptor;
 
 void time_AP(ParCSRMatrix* A, ParCSRMatrix* P, int n_tests, bool tap, const char* name)
 {
diff --git a/examples/profile_amg.cpp b/examples/profile_amg.cpp
index fb2c65e8..9434ef82 100644
--- a/examples/profile_amg.cpp
+++ b/examples/profile_amg.cpp
@@ -10,6 +10,7 @@
 
 #include "raptor/raptor.hpp"
 
+using namespace raptor;
 int main(int argc, char* argv[])
 {
     MPI_Init(&argc, &argv);
diff --git a/examples/profile_rss.cpp b/examples/profile_rss.cpp
index cd21f0ff..474c10fd 100644
--- a/examples/profile_rss.cpp
+++ b/examples/profile_rss.cpp
@@ -8,18 +8,18 @@
 
 #include "clear_cache.hpp"
 
-#include "core/par_matrix.hpp"
-#include "core/par_vector.hpp"
-#include "core/types.hpp"
-#include "gallery/par_stencil.hpp"
-#include "gallery/laplacian27pt.hpp"
-#include "gallery/diffusion.hpp"
-#include "gallery/par_matrix_IO.hpp"
-#include "multilevel/par_multilevel.hpp"
-#include "ruge_stuben/par_ruge_stuben_solver.hpp"
+#include "raptor/core/par_matrix.hpp"
+#include "raptor/core/par_vector.hpp"
+#include "raptor/core/types.hpp"
+#include "raptor/gallery/par_stencil.hpp"
+#include "raptor/gallery/laplacian27pt.hpp"
+#include "raptor/gallery/diffusion.hpp"
+#include "raptor/gallery/par_matrix_IO.hpp"
+#include "raptor/multilevel/par_multilevel.hpp"
+#include "raptor/ruge_stuben/par_ruge_stuben_solver.hpp"
 
 #ifdef USING_MFEM
-#include "external/mfem_wrapper.hpp"
+#include "raptor/external/mfem_wrapper.hpp"
 #endif
 
 using namespace raptor;
diff --git a/examples/profile_tap_amg.cpp b/examples/profile_tap_amg.cpp
index 32734124..66fffa96 100644
--- a/examples/profile_tap_amg.cpp
+++ b/examples/profile_tap_amg.cpp
@@ -10,6 +10,7 @@
 
 #include "raptor/raptor.hpp"
 
+using namespace raptor;
 
 int main(int argc, char* argv[])
 {
diff --git a/examples/profile_tap_rss.cpp b/examples/profile_tap_rss.cpp
index bd2a1cd2..e31103e4 100644
--- a/examples/profile_tap_rss.cpp
+++ b/examples/profile_tap_rss.cpp
@@ -10,6 +10,8 @@
 
 #include "raptor/raptor.hpp"
 
+using namespace raptor;
+
 int main(int argc, char* argv[])
 {
     MPI_Init(&argc, &argv);
diff --git a/examples/profile_tap_sas.cpp b/examples/profile_tap_sas.cpp
index 7589a8be..e9c3c3cb 100644
--- a/examples/profile_tap_sas.cpp
+++ b/examples/profile_tap_sas.cpp
@@ -10,6 +10,8 @@
 
 #include "raptor/raptor.hpp"
 
+using namespace raptor;
+
 int main(int argc, char* argv[])
 {
     MPI_Init(&argc, &argv);
diff --git a/examples/profile_tap_spgemm.cpp b/examples/profile_tap_spgemm.cpp
index c791dd34..79e70cfc 100644
--- a/examples/profile_tap_spgemm.cpp
+++ b/examples/profile_tap_spgemm.cpp
@@ -8,24 +8,26 @@
 
 #include "clear_cache.hpp"
 
-#include "core/par_matrix.hpp"
-#include "core/par_vector.hpp"
-#include "core/types.hpp"
-#include "gallery/par_stencil.hpp"
-#include "gallery/laplacian27pt.hpp"
-#include "gallery/diffusion.hpp"
-#include "gallery/par_matrix_IO.hpp"
-#include "multilevel/par_multilevel.hpp"
-#include "ruge_stuben/par_ruge_stuben_solver.hpp"
+#include "raptor/core/par_matrix.hpp"
+#include "raptor/core/par_vector.hpp"
+#include "raptor/core/types.hpp"
+#include "raptor/gallery/par_stencil.hpp"
+#include "raptor/gallery/laplacian27pt.hpp"
+#include "raptor/gallery/diffusion.hpp"
+#include "raptor/gallery/par_matrix_IO.hpp"
+#include "raptor/multilevel/par_multilevel.hpp"
+#include "raptor/ruge_stuben/par_ruge_stuben_solver.hpp"
 
 #ifdef USING_MFEM
-  #include "external/mfem_wrapper.hpp"
+  #include "raptor/external/mfem_wrapper.hpp"
 #endif
 
 
 #define eager_cutoff 1000
 #define short_cutoff 62
 
+using namespace raptor;
+
 int main(int argc, char *argv[])
 {
     MPI_Init(&argc, &argv);
diff --git a/examples/profile_tap_steps.cpp b/examples/profile_tap_steps.cpp
index f8f6aff8..9bbbfc9a 100644
--- a/examples/profile_tap_steps.cpp
+++ b/examples/profile_tap_steps.cpp
@@ -10,6 +10,7 @@
 
 #include "raptor/raptor.hpp"
 
+using namespace raptor;
 
 void time_AP(ParCSRMatrix* A, ParCSRMatrix* P, int n_tests, bool tap, const char* name)
 {
diff --git a/examples/test_tap.cpp b/examples/test_tap.cpp
index 22c16d93..2bcf5168 100644
--- a/examples/test_tap.cpp
+++ b/examples/test_tap.cpp
@@ -8,19 +8,19 @@
 
 #include "clear_cache.hpp"
 
-#include "core/par_matrix.hpp"
-#include "core/par_vector.hpp"
-#include "core/types.hpp"
-#include "gallery/par_stencil.hpp"
-#include "gallery/laplacian27pt.hpp"
-#include "gallery/diffusion.hpp"
-#include "gallery/par_matrix_IO.hpp"
+#include "raptor/core/par_matrix.hpp"
+#include "raptor/core/par_vector.hpp"
+#include "raptor/core/types.hpp"
+#include "raptor/gallery/par_stencil.hpp"
+#include "raptor/gallery/laplacian27pt.hpp"
+#include "raptor/gallery/diffusion.hpp"
+#include "raptor/gallery/par_matrix_IO.hpp"
 
 #ifdef USING_MFEM
-#include "external/mfem_wrapper.hpp"
+#include "raptor/external/mfem_wrapper.hpp"
 #endif
 
-//using namespace raptor;
+using namespace raptor;
 int main(int argc, char *argv[])
 {
     MPI_Init(&argc, &argv);
diff --git a/raptor/aggregation/aggregate.cpp b/raptor/aggregation/aggregate.cpp
index 7fab0933..0829d918 100644
--- a/raptor/aggregation/aggregate.cpp
+++ b/raptor/aggregation/aggregate.cpp
@@ -2,6 +2,7 @@
 // License: Simplified BSD, http://opensource.org/licenses/BSD-2-Clause
 #include "aggregate.hpp"
 
+namespace raptor {
 int aggregate(CSRMatrix* A, CSRMatrix* S, std::vector<int>& states,
         std::vector<int>& aggregates, double* rand_vals)
 {
@@ -93,3 +94,4 @@ int aggregate(CSRMatrix* A, CSRMatrix* S, std::vector<int>& states,
 
     return n_aggs;
 }
+}
diff --git a/raptor/aggregation/aggregate.hpp b/raptor/aggregation/aggregate.hpp
index 856c607b..1c8754e1 100644
--- a/raptor/aggregation/aggregate.hpp
+++ b/raptor/aggregation/aggregate.hpp
@@ -7,11 +7,10 @@
 #include "raptor/core/matrix.hpp"
 #include "mis.hpp"
 
-using namespace raptor;
+namespace raptor {
 
 int aggregate(CSRMatrix* A, CSRMatrix* S, std::vector<int>& states,
         std::vector<int>& aggregates, double* rand_vals = NULL);
 
+}
 #endif
-
-
diff --git a/raptor/aggregation/candidates.cpp b/raptor/aggregation/candidates.cpp
index e9a09f91..a2bde24b 100644
--- a/raptor/aggregation/candidates.cpp
+++ b/raptor/aggregation/candidates.cpp
@@ -2,6 +2,8 @@
 // License: Simplified BSD, http://opensource.org/licenses/BSD-2-Clause
 #include "candidates.hpp"
 
+namespace raptor {
+
 CSRMatrix* fit_candidates(const int n_aggs, const std::vector<int>& aggregates, 
         const std::vector<double>& B, std::vector<double>& R,
         int num_candidates, double tol)
@@ -135,3 +137,5 @@ CSRMatrix* fit_candidates(const int n_aggs, const std::vector<int>& aggregates,
 
     return T;
 }
+
+}
diff --git a/raptor/aggregation/candidates.hpp b/raptor/aggregation/candidates.hpp
index 06581471..d0e79ef1 100644
--- a/raptor/aggregation/candidates.hpp
+++ b/raptor/aggregation/candidates.hpp
@@ -6,10 +6,10 @@
 #include "raptor/core/types.hpp"
 #include "raptor/core/matrix.hpp"
 
-using namespace raptor;
-
+namespace raptor {
 // TODO -- currently only accepts constant vector
 CSRMatrix* fit_candidates(const int n_aggs, const std::vector<int>& aggregates, 
         const std::vector<double>& B, std::vector<double>& R,
         int num_candidates, double tol = 1e-10);
+}
 #endif
diff --git a/raptor/aggregation/mis.cpp b/raptor/aggregation/mis.cpp
index c9f5c6d0..bb435a25 100644
--- a/raptor/aggregation/mis.cpp
+++ b/raptor/aggregation/mis.cpp
@@ -2,6 +2,8 @@
 // License: Simplified BSD, http://opensource.org/licenses/BSD-2-Clause
 #include "mis.hpp"
 
+namespace raptor {
+
 void mis2(CSRMatrix* A, std::vector<int>& states,
         double* rand_vals)
 {
@@ -217,3 +219,4 @@ void mis2(CSRMatrix* A, std::vector<int>& states,
     delete A_csc;
 }
 
+}
diff --git a/raptor/aggregation/mis.hpp b/raptor/aggregation/mis.hpp
index 9d3e6f8a..a9417211 100644
--- a/raptor/aggregation/mis.hpp
+++ b/raptor/aggregation/mis.hpp
@@ -6,9 +6,10 @@
 #include "raptor/core/types.hpp"
 #include "raptor/core/matrix.hpp"
 
-using namespace raptor;
+namespace raptor {
 
 void mis2(CSRMatrix* A, std::vector<int>& states,
         double* rand_vals = NULL);
 
+}
 #endif
diff --git a/raptor/aggregation/par_aggregate.cpp b/raptor/aggregation/par_aggregate.cpp
index b9e5f38a..ced848be 100644
--- a/raptor/aggregation/par_aggregate.cpp
+++ b/raptor/aggregation/par_aggregate.cpp
@@ -2,6 +2,8 @@
 // License: Simplified BSD, http://opensource.org/licenses/BSD-2-Clause
 #include "par_aggregate.hpp"
 
+namespace raptor {
+
 int aggregate(ParCSRMatrix* A, ParCSRMatrix* S, std::vector<int>& states,
         std::vector<int>& off_proc_states, std::vector<int>& aggregates,
         bool tap_comm, double* rand_vals)
@@ -166,7 +168,7 @@ int aggregate(ParCSRMatrix* A, ParCSRMatrix* S, std::vector<int>& states,
                     max_agg = off_proc_aggregates[col];
                 }
             }
-            
+
             aggregates[i] = - (max_agg + 1);
         }
     }
@@ -182,3 +184,4 @@ int aggregate(ParCSRMatrix* A, ParCSRMatrix* S, std::vector<int>& states,
     return n_aggs;
 }
 
+}
diff --git a/raptor/aggregation/par_aggregate.hpp b/raptor/aggregation/par_aggregate.hpp
index 5ee3b32c..9a5ada41 100644
--- a/raptor/aggregation/par_aggregate.hpp
+++ b/raptor/aggregation/par_aggregate.hpp
@@ -7,12 +7,13 @@
 #include "raptor/core/par_matrix.hpp"
 #include "par_mis.hpp"
 
-using namespace raptor;
+namespace raptor {
 
 int aggregate(ParCSRMatrix* A, ParCSRMatrix* S, std::vector<int>& states,
         std::vector<int>& off_proc_states, std::vector<int>& aggregates,
         bool tap_comm = false, double* rand_vals = NULL);
 
+}
 #endif
 
 
diff --git a/raptor/aggregation/par_candidates.cpp b/raptor/aggregation/par_candidates.cpp
index 498981dc..4f0602e1 100644
--- a/raptor/aggregation/par_candidates.cpp
+++ b/raptor/aggregation/par_candidates.cpp
@@ -2,6 +2,7 @@
 // License: Simplified BSD, http://opensource.org/licenses/BSD-2-Clause
 #include "par_candidates.hpp"
 
+namespace raptor {
 // TODO -- currently assumes B with single candidate
 ParCSRMatrix* fit_candidates(ParCSRMatrix* A, 
         const int n_aggs, const std::vector<int>& aggregates, 
@@ -206,8 +207,4 @@ ParCSRMatrix* fit_candidates(ParCSRMatrix* A,
     return T;
 }
 
-
-
-
-
-
+}
diff --git a/raptor/aggregation/par_candidates.hpp b/raptor/aggregation/par_candidates.hpp
index 54e8a4db..d033acae 100644
--- a/raptor/aggregation/par_candidates.hpp
+++ b/raptor/aggregation/par_candidates.hpp
@@ -6,11 +6,11 @@
 #include "raptor/core/types.hpp"
 #include "raptor/core/par_matrix.hpp"
 
-using namespace raptor;
-
+namespace raptor {
 // TODO -- currently only accepts constant vector
 ParCSRMatrix* fit_candidates(ParCSRMatrix* A, const int n_aggs, 
         const std::vector<int>& aggregates, 
         const std::vector<double>& B, std::vector<double>& R,
         int num_candidates, bool tag_comm = false, double tol = 1e-10);
+}
 #endif
diff --git a/raptor/aggregation/par_mis.cpp b/raptor/aggregation/par_mis.cpp
index bad5e388..71f29193 100644
--- a/raptor/aggregation/par_mis.cpp
+++ b/raptor/aggregation/par_mis.cpp
@@ -2,6 +2,7 @@
 // License: Simplified BSD, http://opensource.org/licenses/BSD-2-Clause
 #include "par_mis.hpp"
 
+namespace raptor {
 // Declare Private Methods
 void comm_states(const ParCSRMatrix* A, CommPkg* comm, 
         const std::vector<int>& states, std::vector<int>& recv_indices, 
@@ -651,3 +652,4 @@ int mis2(const ParCSRMatrix* A, std::vector<int>& states,
     return iterate;
 }
 
+}
diff --git a/raptor/aggregation/par_mis.hpp b/raptor/aggregation/par_mis.hpp
index 5dd03b86..33f854eb 100644
--- a/raptor/aggregation/par_mis.hpp
+++ b/raptor/aggregation/par_mis.hpp
@@ -6,10 +6,11 @@
 #include "raptor/core/types.hpp"
 #include "raptor/core/par_matrix.hpp"
 
-using namespace raptor;
+namespace raptor {
 
 int mis2(const ParCSRMatrix* A, std::vector<int>& states, 
         std::vector<int>& off_proc_states, bool tap_comm = false, 
         double* rand_vals = NULL);
 
+}
 #endif
diff --git a/raptor/aggregation/par_prolongation.cpp b/raptor/aggregation/par_prolongation.cpp
index ba79c153..ea670d3e 100644
--- a/raptor/aggregation/par_prolongation.cpp
+++ b/raptor/aggregation/par_prolongation.cpp
@@ -3,6 +3,7 @@
 
 #include "par_prolongation.hpp"
 
+namespace raptor {
 // Assuming weighting = local (not getting approx spectral radius)
 ParCSRMatrix* jacobi_prolongation(ParCSRMatrix* A, ParCSRMatrix* T, bool tap_comm,
         double omega, int num_smooth_steps)
@@ -102,3 +103,4 @@ ParCSRMatrix* jacobi_prolongation(ParCSRMatrix* A, ParCSRMatrix* T, bool tap_com
     return P;
 }
 
+}
diff --git a/raptor/aggregation/par_prolongation.hpp b/raptor/aggregation/par_prolongation.hpp
index 6c2a142c..c349faa5 100644
--- a/raptor/aggregation/par_prolongation.hpp
+++ b/raptor/aggregation/par_prolongation.hpp
@@ -7,9 +7,9 @@
 #include "raptor/core/par_matrix.hpp"
 #include "raptor/core/par_vector.hpp"
 
-using namespace raptor;
-
+namespace raptor {
 ParCSRMatrix* jacobi_prolongation(ParCSRMatrix* A, ParCSRMatrix* T, bool tap_comm = false,
         double omega = 4.0/3, int num_smooth_steps = 1);
+}
 #endif
 
diff --git a/raptor/aggregation/prolongation.cpp b/raptor/aggregation/prolongation.cpp
index 859bfc69..34eaf4be 100644
--- a/raptor/aggregation/prolongation.cpp
+++ b/raptor/aggregation/prolongation.cpp
@@ -3,6 +3,7 @@
 
 #include "prolongation.hpp"
 
+namespace raptor {
 // Assuming weighting = local (not getting approx spectral radius)
 CSRMatrix* jacobi_prolongation(CSRMatrix* A, CSRMatrix* T, double omega, 
         int num_smooth_steps)
@@ -52,3 +53,4 @@ CSRMatrix* jacobi_prolongation(CSRMatrix* A, CSRMatrix* T, double omega,
     
     return P;
 }
+}
diff --git a/raptor/aggregation/prolongation.hpp b/raptor/aggregation/prolongation.hpp
index aa4610e4..8394b565 100644
--- a/raptor/aggregation/prolongation.hpp
+++ b/raptor/aggregation/prolongation.hpp
@@ -7,8 +7,8 @@
 #include "raptor/core/matrix.hpp"
 #include "raptor/core/vector.hpp"
 
-using namespace raptor;
-
+namespace raptor {
 CSRMatrix* jacobi_prolongation(CSRMatrix* A, CSRMatrix* T, double omega = 4.0/3, 
         int num_smooth_steps = 1);
+}
 #endif
diff --git a/raptor/core/types.hpp b/raptor/core/types.hpp
index 5408b2b6..850a4627 100644
--- a/raptor/core/types.hpp
+++ b/raptor/core/types.hpp
@@ -21,8 +21,6 @@
 #include <vector>
 #include <stdexcept>
 
-using namespace std;
-
 #define zero_tol 1e-16
 #define RAPtor_MPI_INDEX_T MPI_INT
 #define RAPtor_MPI_DATA_T MPI_DOUBLE
@@ -38,7 +36,7 @@ using namespace std;
 
 
 // Global Timing Variables
-struct PairData 
+struct PairData
 {
     double val;
     int index;
@@ -56,7 +54,7 @@ namespace raptor
     enum prolong_t {JacobiProlongation};
     enum relax_t {Jacobi, SOR, SSOR};
 
-    template<typename T, typename U> 
+    template<typename T, typename U>
     U sum_func(const U& a, const T&b)
     {
         return a + b;
diff --git a/raptor/external/hypre_wrapper.cpp b/raptor/external/hypre_wrapper.cpp
index fca760af..39e52867 100644
--- a/raptor/external/hypre_wrapper.cpp
+++ b/raptor/external/hypre_wrapper.cpp
@@ -4,6 +4,8 @@
 
 #include "hypre_wrapper.hpp"
 
+using namespace raptor;
+
 HYPRE_IJVector convert(raptor::ParVector& x_rap, RAPtor_MPI_Comm comm_mat)
 {
     int num_procs, rank;
diff --git a/raptor/external/hypre_wrapper.hpp b/raptor/external/hypre_wrapper.hpp
index b38090d0..ae354d0c 100644
--- a/raptor/external/hypre_wrapper.hpp
+++ b/raptor/external/hypre_wrapper.hpp
@@ -12,8 +12,6 @@
 #include "_hypre_parcsr_mv.h"
 #include "_hypre_parcsr_ls.h"
 
-using namespace raptor;
-
 HYPRE_IJVector convert(raptor::ParVector& x_rap,
                        RAPtor_MPI_Comm comm_mat = RAPtor_MPI_COMM_WORLD);
 HYPRE_IJMatrix convert(raptor::ParCSRMatrix* A_rap,
diff --git a/raptor/external/mfem_wrapper.hpp b/raptor/external/mfem_wrapper.hpp
index c09f8146..b8eeae1b 100644
--- a/raptor/external/mfem_wrapper.hpp
+++ b/raptor/external/mfem_wrapper.hpp
@@ -4,49 +4,47 @@
 #ifndef RAPTOR_MFEM_WRAPPER_H
 #define RAPTOR_MFEM_WRAPPER_H
 
-#include "external/hypre_wrapper.hpp"
-#include "core/types.hpp"
-#include "core/par_matrix.hpp"
-#include "core/par_vector.hpp"
+#include "raptor/external/hypre_wrapper.hpp"
+#include "raptor/core/types.hpp"
+#include "raptor/core/par_matrix.hpp"
+#include "raptor/core/par_vector.hpp"
 #include "mfem.hpp"
 #include <fstream>
 #include <iostream>
 
-using namespace std;
-
-raptor::ParCSRMatrix* mfem_linear_elasticity(raptor::ParVector& x_raptor, 
+raptor::ParCSRMatrix* mfem_linear_elasticity(raptor::ParVector& x_raptor,
         raptor::ParVector& b_raptor, int* num_variables,
-        const char* mesh_file, 
+        const char* mesh_file,
         int order = 3, int seq_n_refines = 2, int par_n_refines = 2,
         RAPtor_MPI_Comm comm_mat = RAPtor_MPI_COMM_WORLD);
 
-raptor::ParCSRMatrix* mfem_dg_elasticity(raptor::ParVector& x_raptor, 
+raptor::ParCSRMatrix* mfem_dg_elasticity(raptor::ParVector& x_raptor,
         raptor::ParVector& b_raptor, int* num_variables,
-        const char* mesh_file, 
+        const char* mesh_file,
         int order = 3, int seq_n_refines = 2, int par_n_refines = 2,
         RAPtor_MPI_Comm comm_mat = RAPtor_MPI_COMM_WORLD);
 
-raptor::ParCSRMatrix* mfem_grad_div(raptor::ParVector& x_raptor, 
+raptor::ParCSRMatrix* mfem_grad_div(raptor::ParVector& x_raptor,
         raptor::ParVector& b_raptor,
-        const char* mesh_file, 
+        const char* mesh_file,
         int order = 3, int seq_n_refines = 2, int par_n_refines = 2,
         RAPtor_MPI_Comm comm_mat = RAPtor_MPI_COMM_WORLD);
 
-raptor::ParCSRMatrix* mfem_adaptive_laplacian(raptor::ParVector& x_raptor, 
+raptor::ParCSRMatrix* mfem_adaptive_laplacian(raptor::ParVector& x_raptor,
         raptor::ParVector& b_raptor,
-        const char* mesh_file, 
+        const char* mesh_file,
         int order = 3, int max_dofs = 1000000,
         RAPtor_MPI_Comm comm_mat = RAPtor_MPI_COMM_WORLD);
 
-raptor::ParCSRMatrix* mfem_dg_diffusion(raptor::ParVector& x_raptor, 
+raptor::ParCSRMatrix* mfem_dg_diffusion(raptor::ParVector& x_raptor,
         raptor::ParVector& b_raptor,
-        const char* mesh_file, 
+        const char* mesh_file,
         int order = 3, int seq_n_refines = 2, int par_n_refines = 2,
         RAPtor_MPI_Comm comm_mat = RAPtor_MPI_COMM_WORLD);
 
-raptor::ParCSRMatrix* mfem_laplacian(raptor::ParVector& x_raptor, 
+raptor::ParCSRMatrix* mfem_laplacian(raptor::ParVector& x_raptor,
         raptor::ParVector& b_raptor,
-        const char* mesh_file, 
+        const char* mesh_file,
         int order = 3, int seq_n_refines = 2, int par_n_refines = 2,
         RAPtor_MPI_Comm comm_mat = RAPtor_MPI_COMM_WORLD);
 
diff --git a/raptor/gallery/diffusion.cpp b/raptor/gallery/diffusion.cpp
index 88da3414..470fd626 100644
--- a/raptor/gallery/diffusion.cpp
+++ b/raptor/gallery/diffusion.cpp
@@ -3,6 +3,7 @@
 
 #include "diffusion.hpp"
 
+namespace raptor {
 // diffusion_stencil_2d
 //
 // Generate a diffusion stencil
@@ -79,3 +80,4 @@ data_t* diffusion_stencil_2d(data_t eps, data_t theta)
     return stencil;
 }
 
+}
diff --git a/raptor/gallery/diffusion.hpp b/raptor/gallery/diffusion.hpp
index dea7385e..bc49904a 100644
--- a/raptor/gallery/diffusion.hpp
+++ b/raptor/gallery/diffusion.hpp
@@ -6,8 +6,7 @@
 
 #include "raptor/core/types.hpp"
 
-using namespace raptor;
-
+namespace raptor {
 // diffusion_stencil_2d
 //
 // Generate a diffusion stencil
@@ -57,5 +56,6 @@ using namespace raptor;
 //
 data_t* diffusion_stencil_2d(data_t eps = 1.0, data_t theta = 0.0);
 
+}
 
 #endif
diff --git a/raptor/gallery/laplacian27pt.cpp b/raptor/gallery/laplacian27pt.cpp
index 263e958b..012037a3 100644
--- a/raptor/gallery/laplacian27pt.cpp
+++ b/raptor/gallery/laplacian27pt.cpp
@@ -3,6 +3,7 @@
 
 #include "laplacian27pt.hpp"
 
+namespace raptor {
 // 27 Point Laplacian Stencil
 //
 // Generate a 27-point laplacian stencil
@@ -32,3 +33,4 @@ data_t* laplace_stencil_27pt()
     return stencil;
 }
 
+}
diff --git a/raptor/gallery/laplacian27pt.hpp b/raptor/gallery/laplacian27pt.hpp
index e1366d17..3a843ec2 100644
--- a/raptor/gallery/laplacian27pt.hpp
+++ b/raptor/gallery/laplacian27pt.hpp
@@ -7,7 +7,7 @@
 #include "raptor/core/types.hpp"
 #include <stdlib.h>
 
-using namespace raptor;
+namespace raptor {
 
 // 27 Point Laplacian Stencil
 //
@@ -26,4 +26,5 @@ using namespace raptor;
 
 data_t* laplace_stencil_27pt();
 
+}
 #endif
diff --git a/raptor/gallery/matrix_IO.cpp b/raptor/gallery/matrix_IO.cpp
index e8a9a827..e1eb166c 100644
--- a/raptor/gallery/matrix_IO.cpp
+++ b/raptor/gallery/matrix_IO.cpp
@@ -23,6 +23,7 @@ void endian_swap(T *objp)
 }
 }
 
+namespace raptor {
 CSRMatrix* readMatrix(const char* filename)
 {
     CSRMatrix* A;
@@ -88,7 +89,7 @@ CSRMatrix* readMatrix(const char* filename)
             ifs.read(reinterpret_cast<char *>(&idx), sizeof_int32);
             displ += idx;
             A->idx1[i+1] = displ;
-        }   
+        }
         for (int32_t i = 0; i < nnz; i++)
         {
             ifs.read(reinterpret_cast<char *>(&idx), sizeof_int32);
@@ -106,7 +107,6 @@ CSRMatrix* readMatrix(const char* filename)
     ifs.close();
 
     return A;
-    
-}
-
 
+}
+}
diff --git a/raptor/gallery/matrix_IO.hpp b/raptor/gallery/matrix_IO.hpp
index 807f52f5..b48e1578 100644
--- a/raptor/gallery/matrix_IO.hpp
+++ b/raptor/gallery/matrix_IO.hpp
@@ -15,9 +15,10 @@
 #include "raptor/core/matrix.hpp"
 #include "raptor/core/types.hpp"
 
-using namespace raptor;
+namespace raptor {
 
 CSRMatrix* readMatrix(const char* filename);
 
+}
 #endif
 
diff --git a/raptor/gallery/matrix_market.cpp b/raptor/gallery/matrix_market.cpp
index 9454408f..822ac102 100644
--- a/raptor/gallery/matrix_market.cpp
+++ b/raptor/gallery/matrix_market.cpp
@@ -13,7 +13,7 @@
 
 #include "matrix_market.hpp"
 
-using namespace raptor;
+namespace raptor {
 
 // Declare Private Methods
 char *mm_strdup(const char *s);
@@ -535,3 +535,4 @@ char  *mm_typecode_to_str(MM_typecode matcode)
 
 }
 
+}
diff --git a/raptor/gallery/matrix_market.hpp b/raptor/gallery/matrix_market.hpp
index b8c9bd38..93791036 100644
--- a/raptor/gallery/matrix_market.hpp
+++ b/raptor/gallery/matrix_market.hpp
@@ -11,7 +11,8 @@
 
 #include "raptor/core/types.hpp"
 #include "raptor/core/matrix.hpp"
-using namespace raptor;
+
+namespace raptor {
 
 #define MM_MAX_LINE_LENGTH 1025
 #define MatrixMarketBanner "%%MatrixMarket"
@@ -119,7 +120,6 @@ int mm_is_valid(MM_typecode matcode);		/* too complex for a macro */
 #define MM_SKEW_STR		"skew-symmetric"
 #define MM_PATTERN_STR  "pattern"
 
-
 /*  high level routines */
 
 int mm_write_mtx_crd(char fname[], int M, int N, int nz, int I[], int J[],
@@ -132,7 +132,6 @@ int mm_read_mtx_crd_entry(FILE *f, int *I, int *J, double *real, double *img,
 CSRMatrix* read_mm(const char* fname);
 void write_mm(CSRMatrix* A, const char* fname);
 
+}
 
 #endif
-
-
diff --git a/raptor/gallery/par_matrix_IO.cpp b/raptor/gallery/par_matrix_IO.cpp
index 7d80d131..1b96d750 100644
--- a/raptor/gallery/par_matrix_IO.cpp
+++ b/raptor/gallery/par_matrix_IO.cpp
@@ -21,6 +21,7 @@ void endian_swap(T *objp)
 }
 }
 
+namespace raptor {
 ParCSRMatrix* readParMatrix(const char* filename, 
         int local_num_rows, int local_num_cols,
         int first_local_row, int first_local_col, 
@@ -183,3 +184,4 @@ ParCSRMatrix* readParMatrix(const char* filename,
 
     return A;
 }
+}
diff --git a/raptor/gallery/par_matrix_IO.hpp b/raptor/gallery/par_matrix_IO.hpp
index 25fa7fef..a5ea6ef2 100644
--- a/raptor/gallery/par_matrix_IO.hpp
+++ b/raptor/gallery/par_matrix_IO.hpp
@@ -15,12 +15,12 @@
 #include "raptor/core/par_matrix.hpp"
 #include "raptor/core/types.hpp"
 
-using namespace raptor;
+namespace raptor {
 
 ParCSRMatrix* readParMatrix(const char* filename, 
         int local_num_rows = -1, int local_num_cols = -1,
         int first_local_row = -1, int first_local_col = -1, 
         RAPtor_MPI_Comm comm = RAPtor_MPI_COMM_WORLD);
 
+}
 #endif
-
diff --git a/raptor/gallery/par_matrix_market.cpp b/raptor/gallery/par_matrix_market.cpp
index 7f9830cf..eabcd962 100644
--- a/raptor/gallery/par_matrix_market.cpp
+++ b/raptor/gallery/par_matrix_market.cpp
@@ -1,4 +1,4 @@
-/* 
+/*
 *   Matrix Market I/O library for ANSI C
 *
 *   See http://math.nist.gov/MatrixMarket for details.
@@ -13,7 +13,7 @@
 
 #include "par_matrix_market.hpp"
 
-using namespace raptor;
+namespace raptor {
 
 // Declare Private Methods
 void write_par_data(FILE* f, int n, int* rowptr, int* col_idx,
@@ -28,19 +28,19 @@ ParCSRMatrix* read_par_mm(const char *fname)
     int row, col;
     int n_items_read;
     double val;
- 
+
     if ((f = fopen(fname, "r")) == NULL)
             return NULL;
- 
- 
+
+
     if (mm_read_banner(f, &matcode) != 0)
     {
         printf("mm_read_unsymetric: Could not process Matrix Market banner ");
         printf(" in file [%s]\n", fname);
         return NULL;
     }
- 
- 
+
+
     if ( !(mm_is_real(matcode) && mm_is_matrix(matcode) &&
             mm_is_sparse(matcode)))
     {
@@ -49,15 +49,15 @@ ParCSRMatrix* read_par_mm(const char *fname)
                 mm_typecode_to_str(matcode));
         return NULL;
     }
- 
+
     /* find out size of sparse matrix: M, N, nz .... */
- 
+
     if (mm_read_mtx_crd_size(f, &M, &N, &nz) !=0)
     {
         fprintf(stderr, "read_unsymmetric_sparse(): could not parse matrix size.\n");
         return NULL;
     }
- 
+
     int row_nnz = nz / M;
     ParCOOMatrix* A = new ParCOOMatrix(M, N);
     A->on_proc->vals.reserve(row_nnz);
@@ -66,7 +66,7 @@ ParCSRMatrix* read_par_mm(const char *fname)
     /* NOTE: when reading in doubles, ANSI C requires the use of the "l"  */
     /*   specifier as in "%lg", "%lf", "%le", otherwise errors will occur */
     /*  (ANSI C X3.159-1989, Sec. 4.9.6.2, p. 136 lines 13-15)            */
- 
+
     bool symmetric = mm_is_symmetric(matcode);
     bool row_local;
     bool col_local;
@@ -84,7 +84,7 @@ ParCSRMatrix* read_par_mm(const char *fname)
         else
         {
             row_local = false;
-            if (!symmetric) 
+            if (!symmetric)
                 continue;
         }
         if (col >= A->partition->first_local_col && col <= A->partition->last_local_col)
@@ -95,7 +95,7 @@ ParCSRMatrix* read_par_mm(const char *fname)
         else
         {
             col_local = false;
-            if (!row_local) 
+            if (!row_local)
                 continue;
         }
 
@@ -132,7 +132,7 @@ ParCSRMatrix* read_par_mm(const char *fname)
     delete A;
 
     fclose(f);
- 
+
     return A_csr;
 }
 
@@ -148,7 +148,7 @@ void write_par_data(FILE* f, int n, int* rowptr, int* col_idx,
         end = rowptr[i+1];
         for (int j = start; j < end; j++)
         {
-            fprintf(f, "%d %d %2.15e\n", global_row + 1, 
+            fprintf(f, "%d %d %2.15e\n", global_row + 1,
                     col_map[col_idx[j]] + 1, vals[j]);
         }
     }
@@ -178,7 +178,7 @@ void write_par_mm(ParCSRMatrix* A, const char *fname)
     int dims[5];
     dims[0] = A->local_num_rows + 1;
     dims[1] = A->on_proc_num_cols;
-    dims[2] = A->off_proc_num_cols; 
+    dims[2] = A->off_proc_num_cols;
     dims[3] = A->on_proc->nnz;
     dims[4] = A->off_proc->nnz;
     RAPtor_MPI_Gather(dims, 5, RAPtor_MPI_INT, proc_dims.data(), 5, RAPtor_MPI_INT, 0, RAPtor_MPI_COMM_WORLD);
@@ -212,7 +212,7 @@ void write_par_mm(ParCSRMatrix* A, const char *fname)
         std::vector<int> idx2;
         std::vector<double> vals;
         std::vector<int> row_map;
-        std::vector<int> col_map; 
+        std::vector<int> col_map;
         for (int i = 1; i < num_procs; i++)
         {
             // Calculate comm_size and allocate recv_buf
@@ -252,7 +252,7 @@ void write_par_mm(ParCSRMatrix* A, const char *fname)
                     RAPtor_MPI_INT, RAPtor_MPI_COMM_WORLD);
             RAPtor_MPI_Unpack(buffer.data(), comm_size, &pos, vals.data(), i_dims[3],
                     RAPtor_MPI_DOUBLE, RAPtor_MPI_COMM_WORLD);
-            write_par_data(f, i_dims[0] - 1, idx1.data(), idx2.data(), 
+            write_par_data(f, i_dims[0] - 1, idx1.data(), idx2.data(),
                     vals.data(), first_row, col_map.data());
 
             RAPtor_MPI_Unpack(buffer.data(), comm_size, &pos, col_map.data(), i_dims[2],
@@ -263,7 +263,7 @@ void write_par_mm(ParCSRMatrix* A, const char *fname)
                     RAPtor_MPI_INT, RAPtor_MPI_COMM_WORLD);
             RAPtor_MPI_Unpack(buffer.data(), comm_size, &pos, vals.data(), i_dims[4],
                     RAPtor_MPI_DOUBLE, RAPtor_MPI_COMM_WORLD);
-            write_par_data(f, i_dims[0] - 1, idx1.data(), idx2.data(), 
+            write_par_data(f, i_dims[0] - 1, idx1.data(), idx2.data(),
                     vals.data(), first_row, col_map.data());
 
             first_row += i_dims[0] - 1;
@@ -283,17 +283,17 @@ void write_par_mm(ParCSRMatrix* A, const char *fname)
 
         // Pack Data
         pos = 0;
-        RAPtor_MPI_Pack(A->on_proc_column_map.data(), dims[1], RAPtor_MPI_INT, buffer.data(), comm_size, 
-               &pos, RAPtor_MPI_COMM_WORLD); 
+        RAPtor_MPI_Pack(A->on_proc_column_map.data(), dims[1], RAPtor_MPI_INT, buffer.data(), comm_size,
+               &pos, RAPtor_MPI_COMM_WORLD);
         RAPtor_MPI_Pack(A->on_proc->idx1.data(), dims[0], RAPtor_MPI_INT, buffer.data(), comm_size,
                 &pos, RAPtor_MPI_COMM_WORLD);
         RAPtor_MPI_Pack(A->on_proc->idx2.data(), dims[3], RAPtor_MPI_INT, buffer.data(), comm_size,
                 &pos, RAPtor_MPI_COMM_WORLD);
         RAPtor_MPI_Pack(A->on_proc->vals.data(), dims[3], RAPtor_MPI_DOUBLE, buffer.data(), comm_size,
                 &pos, RAPtor_MPI_COMM_WORLD);
-        
-        RAPtor_MPI_Pack(A->off_proc_column_map.data(), dims[2], RAPtor_MPI_INT, buffer.data(), comm_size, 
-               &pos, RAPtor_MPI_COMM_WORLD); 
+
+        RAPtor_MPI_Pack(A->off_proc_column_map.data(), dims[2], RAPtor_MPI_INT, buffer.data(), comm_size,
+               &pos, RAPtor_MPI_COMM_WORLD);
         RAPtor_MPI_Pack(A->off_proc->idx1.data(), dims[0], RAPtor_MPI_INT, buffer.data(), comm_size,
                 &pos, RAPtor_MPI_COMM_WORLD);
         RAPtor_MPI_Pack(A->off_proc->idx2.data(), dims[4], RAPtor_MPI_INT, buffer.data(), comm_size,
@@ -306,3 +306,4 @@ void write_par_mm(ParCSRMatrix* A, const char *fname)
     }
 }
 
+}
diff --git a/raptor/gallery/par_matrix_market.hpp b/raptor/gallery/par_matrix_market.hpp
index 38cc8b94..5a7af8d5 100644
--- a/raptor/gallery/par_matrix_market.hpp
+++ b/raptor/gallery/par_matrix_market.hpp
@@ -13,13 +13,11 @@
 #include "raptor/core/types.hpp"
 #include "raptor/core/par_matrix.hpp"
 
-using namespace raptor;
+namespace raptor {
 
 /*  high level routines */
 ParCSRMatrix* read_par_mm(const char *fname);
 void write_par_mm(ParCSRMatrix* A, const char *fname);
-
+}
 
 #endif
-
-
diff --git a/raptor/gallery/par_random.cpp b/raptor/gallery/par_random.cpp
index 19fbc10c..bb49d5ce 100644
--- a/raptor/gallery/par_random.cpp
+++ b/raptor/gallery/par_random.cpp
@@ -2,6 +2,7 @@
 // License: Simplified BSD, http://opensource.org/licenses/BSD-2-Clause
 #include "par_random.hpp"
 
+namespace raptor {
 ParCSRMatrix* par_random(int global_rows, int global_cols, int nnz_per_row)
 {
     int rank, num_procs;
@@ -10,7 +11,7 @@ ParCSRMatrix* par_random(int global_rows, int global_cols, int nnz_per_row)
 
     ParCOOMatrix* A_coo;
     double val = 1.0;
-    
+
     A_coo = new ParCOOMatrix(global_rows, global_cols);
     int local_nnz = nnz_per_row * A_coo->local_num_rows;
     for (int i = 0; i < local_nnz; i++)
@@ -26,3 +27,4 @@ ParCSRMatrix* par_random(int global_rows, int global_cols, int nnz_per_row)
 
 }
 
+}
diff --git a/raptor/gallery/par_random.hpp b/raptor/gallery/par_random.hpp
index 2f16a228..1a93a128 100644
--- a/raptor/gallery/par_random.hpp
+++ b/raptor/gallery/par_random.hpp
@@ -12,8 +12,8 @@
 #include "raptor/core/par_matrix.hpp"
 #include "raptor/core/types.hpp"
 
-using namespace raptor;
+namespace raptor {
 
 ParCSRMatrix* par_random(int global_rows, int global_cols, int nnz_per_row);
-
+}
 #endif
diff --git a/raptor/gallery/par_stencil.cpp b/raptor/gallery/par_stencil.cpp
index de801bae..ab18f3a3 100644
--- a/raptor/gallery/par_stencil.cpp
+++ b/raptor/gallery/par_stencil.cpp
@@ -2,6 +2,7 @@
 // License: Simplified BSD, http://opensource.org/licenses/BSD-2-Clause
 #include "par_stencil.hpp"
 
+namespace raptor {
 ParCSRMatrix* par_stencil_grid(data_t* stencil, int* grid, int dim)
 {
     // Get MPI Information
@@ -19,7 +20,7 @@ ParCSRMatrix* par_stencil_grid(data_t* stencil, int* grid, int dim)
     int N_v;  // Number of rows (and cols) in matrix
     int N_s;  // Number of nonzero stencil entries
     int n_v;  // Local number of rows (and cols)
-    
+
     int init_step, idx;
     int len, step, current_step;
     int col;
@@ -101,7 +102,7 @@ ParCSRMatrix* par_stencil_grid(data_t* stencil, int* grid, int dim)
         {
             diags[j] += strides[i] * indices[j][dim-i-1];
         }
-    } 
+    }
 
     //Initial data array
     data.resize(N_s*n_v);
@@ -126,7 +127,7 @@ ParCSRMatrix* par_stencil_grid(data_t* stencil, int* grid, int dim)
     //Zero boundary conditions
     for (index_t i = 0; i < N_s; i++)
     {
-        //get correct chunk of data 
+        //get correct chunk of data
         //(corresponding to single stencil entry)
         init_step = i*n_v;
         for (index_t j = 0; j < dim; j++)
@@ -204,7 +205,7 @@ ParCSRMatrix* par_stencil_grid(data_t* stencil, int* grid, int dim)
     {
         for (index_t d = 0; d < N_s; d++)
         {
-            //add data[i] if nonzero 
+            //add data[i] if nonzero
             col = diags[d] + i + first_local_row;
             value = data[(N_s-d-1)*n_v+i];
             if (col >= 0 && col < N_v && fabs(value) > zero_tol)
@@ -218,10 +219,10 @@ ParCSRMatrix* par_stencil_grid(data_t* stencil, int* grid, int dim)
 
     A->on_proc->nnz = A->on_proc->idx2.size();
     A->off_proc->nnz = A->off_proc->idx2.size();
-    
+
     A->finalize();
 
     return A;
-} 
-
+}
 
+}
diff --git a/raptor/gallery/par_stencil.hpp b/raptor/gallery/par_stencil.hpp
index 72227743..407734b4 100644
--- a/raptor/gallery/par_stencil.hpp
+++ b/raptor/gallery/par_stencil.hpp
@@ -11,10 +11,9 @@
 #include "raptor/core/types.hpp"
 #include "raptor/core/par_matrix.hpp"
 
-using namespace raptor;
+namespace raptor {
 
 ParCSRMatrix* par_stencil_grid(data_t* stencil, int* grid, int dim);
 
+}
 #endif
-
-
diff --git a/raptor/gallery/random.cpp b/raptor/gallery/random.cpp
index 1a9ea0aa..878ce332 100644
--- a/raptor/gallery/random.cpp
+++ b/raptor/gallery/random.cpp
@@ -3,6 +3,7 @@
 
 #include "random.hpp"
 
+namespace raptor {
 CSRMatrix* random(int rows, int cols, int nnz_per_row)
 {
     CSRMatrix* A;
@@ -24,3 +25,4 @@ CSRMatrix* random(int rows, int cols, int nnz_per_row)
 
 }
 
+}
diff --git a/raptor/gallery/random.hpp b/raptor/gallery/random.hpp
index 3ad8177f..166a150f 100644
--- a/raptor/gallery/random.hpp
+++ b/raptor/gallery/random.hpp
@@ -12,8 +12,8 @@
 #include "raptor/core/matrix.hpp"
 #include "raptor/core/types.hpp"
 
-using namespace raptor;
+namespace raptor {
 
 CSRMatrix* random(int rows, int cols, int nnz_per_row);
-
+}
 #endif
diff --git a/raptor/gallery/stencil.cpp b/raptor/gallery/stencil.cpp
index 7eaa04a0..863ec797 100644
--- a/raptor/gallery/stencil.cpp
+++ b/raptor/gallery/stencil.cpp
@@ -3,6 +3,7 @@
 
 #include "stencil.hpp"
 
+namespace raptor {
 // Stencils are symmetric, so A could be CSR or CSC
 CSRMatrix* stencil_grid(data_t* stencil, int* grid, int dim)
 {
@@ -192,3 +193,4 @@ CSRMatrix* stencil_grid(data_t* stencil, int* grid, int dim)
     return A;
 }
 
+}
diff --git a/raptor/gallery/stencil.hpp b/raptor/gallery/stencil.hpp
index debca1f3..4f0c643b 100644
--- a/raptor/gallery/stencil.hpp
+++ b/raptor/gallery/stencil.hpp
@@ -11,10 +11,10 @@
 #include "raptor/core/types.hpp"
 #include "raptor/core/matrix.hpp"
 
-using namespace raptor;
+namespace raptor {
 
 // Stencils are symmetric, so A could be CSR or CSC
 CSRMatrix* stencil_grid(data_t* stencil, int* grid, int dim);
-
+}
 #endif
 
diff --git a/raptor/krylov/bicgstab.cpp b/raptor/krylov/bicgstab.cpp
index 66b3700f..553bb3e6 100644
--- a/raptor/krylov/bicgstab.cpp
+++ b/raptor/krylov/bicgstab.cpp
@@ -2,7 +2,7 @@
 // License: Simplified BSD, http://opensource.org/licenses/BSD-2-Clause
 #include "bicgstab.hpp"
 
-using namespace raptor;
+namespace raptor {
 
 void BiCGStab(CSRMatrix* A, Vector& x, Vector& b, std::vector<double>& res, double tol, int max_iter)
 {
@@ -12,7 +12,7 @@ void BiCGStab(CSRMatrix* A, Vector& x, Vector& b, std::vector<double>& res, doub
     Vector s;
     Vector Ap;
     Vector As;
-    
+
     int iter;
     data_t alpha, beta, omega;
     data_t rrstar_inner, next_rrstar_inner, As_inner, AsAs_inner;
@@ -53,7 +53,7 @@ void BiCGStab(CSRMatrix* A, Vector& x, Vector& b, std::vector<double>& res, doub
     }
 
     iter = 0;
-    
+
     // Main BiCGStab Loop
     while (true)
     {
@@ -76,7 +76,7 @@ void BiCGStab(CSRMatrix* A, Vector& x, Vector& b, std::vector<double>& res, doub
 	x.axpy(s, omega);
 
         // r_{i+1} = s_i - omega_i * As_i
-	r.copy(s);	
+	r.copy(s);
         r.axpy(As, -1.0*omega);
 
         // beta_i = (r_{i+1}, rstar) / (r_i, rstar)
@@ -99,7 +99,7 @@ void BiCGStab(CSRMatrix* A, Vector& x, Vector& b, std::vector<double>& res, doub
 	    return;
 
        	}
-	
+
 	if (iter == max_iter)
 	{
             printf("Max Iterations Reached.\n");
@@ -110,5 +110,4 @@ void BiCGStab(CSRMatrix* A, Vector& x, Vector& b, std::vector<double>& res, doub
 	iter++;
     }
 }
-
-
+}
diff --git a/raptor/krylov/bicgstab.hpp b/raptor/krylov/bicgstab.hpp
index 907e2d83..a0487fea 100644
--- a/raptor/krylov/bicgstab.hpp
+++ b/raptor/krylov/bicgstab.hpp
@@ -7,7 +7,7 @@
 #include "raptor/core/matrix.hpp"
 #include "raptor/core/vector.hpp"
 
-using namespace raptor;
+namespace raptor {
 
 void BiCGStab(CSRMatrix* A, Vector& x, Vector& b, std::vector<double>& res, double tol = 1e-05, int max_iter = -1);
 
@@ -21,5 +21,5 @@ void Test_BiCGStab(CSRMatrix* A, Vector& x, Vector& b, std::vector<double>& res,
 		std::vector<double>& omega_list, std::vector<double>& rr_list, std::vector<double>& beta_list, 
 		std::vector<double>& norm_list, double tol = 1e-05, int max_iter = -1);
 
+}
 #endif
-
diff --git a/raptor/krylov/cg.cpp b/raptor/krylov/cg.cpp
index 36e07fdb..fe8de902 100644
--- a/raptor/krylov/cg.cpp
+++ b/raptor/krylov/cg.cpp
@@ -2,14 +2,14 @@
 // License: Simplified BSD, http://opensource.org/licenses/BSD-2-Clause
 #include "cg.hpp"
 
-using namespace raptor;
+namespace raptor {
 
 void CG(CSRMatrix* A, Vector& x, Vector& b, std::vector<double>& res, double tol, int max_iter)
 {
     Vector r;
     Vector p;
     Vector Ap;
-    
+
     int iter, recompute_r;
     data_t alpha, beta;
     data_t rr_inner, next_inner, App_inner;
@@ -58,7 +58,7 @@ void CG(CSRMatrix* A, Vector& x, Vector& b, std::vector<double>& res, double tol
             exit(-1);
         }
         alpha = rr_inner / App_inner;
-        
+
         x.axpy(p, alpha);
 
         // x_{i+1} = x_i + alpha_i * p_i
@@ -101,3 +101,4 @@ void CG(CSRMatrix* A, Vector& x, Vector& b, std::vector<double>& res, double tol
 
     return;
 }
+}
diff --git a/raptor/krylov/cg.hpp b/raptor/krylov/cg.hpp
index a0296bb0..737d64ac 100644
--- a/raptor/krylov/cg.hpp
+++ b/raptor/krylov/cg.hpp
@@ -7,8 +7,9 @@
 #include "raptor/core/matrix.hpp"
 #include "raptor/core/vector.hpp"
 
-using namespace raptor;
+namespace raptor {
 
 void CG(CSRMatrix* A, Vector& x, Vector& b, std::vector<double>& res, double tol = 1e-05, int max_iter = -1);
 
+}
 #endif
diff --git a/raptor/krylov/par_bicgstab.cpp b/raptor/krylov/par_bicgstab.cpp
index 51484e82..eab6d1a9 100644
--- a/raptor/krylov/par_bicgstab.cpp
+++ b/raptor/krylov/par_bicgstab.cpp
@@ -3,7 +3,7 @@
 #include "par_bicgstab.hpp"
 #include "partial_inner.hpp"
 
-using namespace raptor;
+namespace raptor {
 
 /**************************************************************************************
  BiCGStab 
@@ -892,3 +892,4 @@ void PrePI_BiCGStab(ParCSRMatrix* A, ParVector& x, ParVector& b, std::vector<dou
 */
     return;
 }
+}
diff --git a/raptor/krylov/par_bicgstab.hpp b/raptor/krylov/par_bicgstab.hpp
index 6b6a8f86..64652cb6 100644
--- a/raptor/krylov/par_bicgstab.hpp
+++ b/raptor/krylov/par_bicgstab.hpp
@@ -9,7 +9,7 @@
 #include "raptor/multilevel/par_multilevel.hpp"
 #include "raptor/aggregation/par_smoothed_aggregation_solver.hpp"
 
-using namespace raptor;
+namespace raptor {
 
 void BiCGStab(ParCSRMatrix* A, ParVector& x, ParVector& b, std::vector<double>& res, double tol = 1e-05, int max_iter = -1);
 
@@ -29,4 +29,5 @@ void PI_BiCGStab(ParCSRMatrix* A, ParVector& x, ParVector& b, std::vector<double
 void PrePI_BiCGStab(ParCSRMatrix* A, ParVector& x, ParVector& b, std::vector<double>& res, RAPtor_MPI_Comm &inner_comm,
                  RAPtor_MPI_Comm &root_comm, double frac, int inner_color, int root_color, int inner_root, int procs_in_group,
                  int part_global, double tol = 1e-05, int max_iter = -1);
+}
 #endif
diff --git a/raptor/krylov/par_cg.cpp b/raptor/krylov/par_cg.cpp
index 3289ab57..cea333a7 100644
--- a/raptor/krylov/par_cg.cpp
+++ b/raptor/krylov/par_cg.cpp
@@ -3,7 +3,7 @@
 #include "par_cg.hpp"
 #include "raptor/multilevel/par_multilevel.hpp"
 
-using namespace raptor;
+namespace raptor {
 
 void CG(ParCSRMatrix* A, ParVector& x, ParVector& b, std::vector<double>& res, double tol, int max_iter, double* comm_t)
 {
@@ -262,3 +262,4 @@ if (comm_t) *comm_t += RAPtor_MPI_Wtime();
     return;
 }
 
+}
diff --git a/raptor/krylov/par_cg.hpp b/raptor/krylov/par_cg.hpp
index 25cf928a..5a667671 100644
--- a/raptor/krylov/par_cg.hpp
+++ b/raptor/krylov/par_cg.hpp
@@ -8,7 +8,7 @@
 #include "raptor/core/par_vector.hpp"
 #include "raptor/multilevel/par_multilevel.hpp"
 
-using namespace raptor;
+namespace raptor {
 
 void CG(ParCSRMatrix* A, ParVector& x, ParVector& b, std::vector<double>& res, 
         double tol = 1e-05, int max_iter = -1, double* comm_t = NULL);
@@ -16,4 +16,5 @@ void PCG(ParCSRMatrix* A, ParMultilevel* ml, ParVector& x, ParVector& b,
         std::vector<double>& res, double tol = 1e-05, int max_iter = -1,
         double* precond_t = NULL, double* comm_t = NULL);
 
+}
 #endif
diff --git a/raptor/krylov/partial_inner.cpp b/raptor/krylov/partial_inner.cpp
index 6443a866..3adf7e85 100644
--- a/raptor/krylov/partial_inner.cpp
+++ b/raptor/krylov/partial_inner.cpp
@@ -2,9 +2,9 @@
 // License: Simplified BSD, http://opensource.org/licenses/BSD-2-Clause
 #include "partial_inner.hpp"
 
-using namespace raptor;
+namespace raptor {
 
-/********************************************************************** 
+/**********************************************************************
  Performs approximate inner product using contiguous half of processes
  *********************************************************************/
 data_t half_inner_contig(ParVector &x, ParVector &y, int half, int part_global){
@@ -46,7 +46,7 @@ data_t half_inner_contig(ParVector &x, ParVector &y, int half, int part_global){
 	inner_root = half_procs;
 	recv_root = 0;
     }
-    else{	
+    else{
 	if (rank < half_procs) color = 0;
 	else color = 1;
         inner_root = 0;
@@ -97,8 +97,8 @@ data_t half_inner_contig(ParVector &x, ParVector &y, int half, int part_global){
 }
 
 
-/***************************************************************** 
- Performs sequential inner product for testing reproducibility 
+/*****************************************************************
+ Performs sequential inner product for testing reproducibility
  ****************************************************************/
 data_t sequential_inner(ParVector &x, ParVector &y){
     int rank, num_procs;
@@ -137,8 +137,8 @@ data_t sequential_inner(ParVector &x, ParVector &y){
 }
 
 
-/***************************************************************** 
- Performs sequential vector norm with parallel vector 
+/*****************************************************************
+ Performs sequential vector norm with parallel vector
  ****************************************************************/
 data_t sequential_norm(ParVector &x, index_t p){
     int rank, num_procs;
@@ -171,16 +171,16 @@ void create_partial_inner_comm(RAPtor_MPI_Comm &inner_comm, RAPtor_MPI_Comm &roo
     RAPtor_MPI_Comm_rank(RAPtor_MPI_COMM_WORLD, &rank);
     RAPtor_MPI_Comm_size(RAPtor_MPI_COMM_WORLD, &num_procs);
 
-    if (num_procs <= 1) 
+    if (num_procs <= 1)
     {
        inner_comm = RAPtor_MPI_COMM_NULL;
        root_comm = RAPtor_MPI_COMM_NULL;
        part_global = x.local_n;
-       return; 
+       return;
     }
 
     // Calculate number of processes in group
-    procs_in_group = num_procs * frac; 
+    procs_in_group = num_procs * frac;
     if (num_procs % 2) procs_in_group++;
 
     // Split into contigous groups by color and get root for each group
@@ -202,15 +202,15 @@ void create_partial_inner_comm(RAPtor_MPI_Comm &inner_comm, RAPtor_MPI_Comm &roo
     return;
 }
 
-/***************************************************************** 
+/*****************************************************************
  Performs approximate inner product using half of the processes
  ****************************************************************/
 data_t half_inner(RAPtor_MPI_Comm &inner_comm, ParVector &x, ParVector &y, int &my_color, int send_color, int &inner_root,
                   int &recv_root, int part_global) {
-    /*  inner_comm : MPI communicator containing the processes to use in the inner product 
+    /*  inner_comm : MPI communicator containing the processes to use in the inner product
      *           x : ParVector for calculating inner product
      *           y : ParVector for calculating inner product
-     *    my_color : color corresponding to the procs communicator 
+     *    my_color : color corresponding to the procs communicator
      *  send_color : color calculating the inner product and sending to the other half of processes
      *  inner_root : root of inner_comm
      *   recv_root : root of recv_comm
@@ -234,7 +234,7 @@ data_t half_inner(RAPtor_MPI_Comm &inner_comm, ParVector &x, ParVector &y, int &
         inner_prod = x.local.inner_product(y.local);
         return inner_prod;
     }
-    
+
     // Get communicator sizes
     RAPtor_MPI_Comm_size(inner_comm, &inner_comm_size);
     //MPI_Comm_size(recv_comm, &recv_comm_size);
@@ -275,16 +275,16 @@ data_t half_inner(RAPtor_MPI_Comm &inner_comm, ParVector &x, ParVector &y, int &
     return inner_prod;
 }
 
-/***************************************************************** 
+/*****************************************************************
  Performs approximate inner product using part of the processes
  ****************************************************************/
 data_t partial_inner(RAPtor_MPI_Comm &inner_comm, RAPtor_MPI_Comm &root_comm, ParVector &x, ParVector &y, int my_color,
                      int send_color, int inner_root, int procs_in_group, int part_global) {
-    /*     inner_comm : MPI communicator containing the processes to use in the inner product 
+    /*     inner_comm : MPI communicator containing the processes to use in the inner product
      *      root_comm : MPI communicator containing the root processes for each inner_comm communicator
      *              x : ParVector for calculating inner product
      *              y : ParVector for calculating inner product
-     *       my_color : color corresponding to the processes' communicator 
+     *       my_color : color corresponding to the processes' communicator
      *     send_color : color calculating the inner product and sending to the other processes
      *     inner_root : root of the processes' inner_comm
      * procs_in_group : average number of processes in group - rounded up if uneven
@@ -299,9 +299,9 @@ data_t partial_inner(RAPtor_MPI_Comm &inner_comm, RAPtor_MPI_Comm &root_comm, Pa
 
     // Check if single process or inner_comm undefined - then default to full inner product
     if (num_procs <= 1 || inner_comm == RAPtor_MPI_COMM_NULL){
-        return y.inner_product(x); 
+        return y.inner_product(x);
     }
-    
+
     // Get communicator sizes
     RAPtor_MPI_Comm_size(inner_comm, &inner_comm_size);
 
@@ -334,3 +334,4 @@ data_t partial_inner(RAPtor_MPI_Comm &inner_comm, RAPtor_MPI_Comm &root_comm, Pa
     // Return partial inner_prod scaled by global percentage
     return inner_prod;
 }
+}
diff --git a/raptor/krylov/partial_inner.hpp b/raptor/krylov/partial_inner.hpp
index cbd47f13..36f7ba02 100644
--- a/raptor/krylov/partial_inner.hpp
+++ b/raptor/krylov/partial_inner.hpp
@@ -6,7 +6,7 @@
 #include "raptor/core/types.hpp"
 #include "raptor/core/par_vector.hpp"
 
-using namespace raptor;
+namespace raptor {
 
 data_t half_inner_contig(ParVector &x, ParVector &y, int half, int part_global);
 
@@ -22,4 +22,5 @@ data_t partial_inner(RAPtor_MPI_Comm &inner_comm, RAPtor_MPI_Comm &root_comm, Pa
 data_t sequential_inner(ParVector &x, ParVector &y);
 data_t sequential_norm(ParVector &x, index_t p);
 
+}
 #endif
diff --git a/raptor/multilevel/par_sparsify.hpp b/raptor/multilevel/par_sparsify.hpp
index 268b41b6..014f14a3 100644
--- a/raptor/multilevel/par_sparsify.hpp
+++ b/raptor/multilevel/par_sparsify.hpp
@@ -6,9 +6,10 @@
 #include "raptor/core/types.hpp"
 #include "raptor/core/par_matrix.hpp"
 
-using namespace raptor;
+namespace raptor {
 
 void sparsify(ParCSRMatrix* A, ParCSRMatrix* P, ParCSRMatrix* I, 
         ParCSRMatrix* AP, ParCSRMatrix* Ac, const double theta = 0.1);
 
+}
 #endif
diff --git a/raptor/ruge_stuben/cf_splitting.cpp b/raptor/ruge_stuben/cf_splitting.cpp
index 65d9311f..a5742081 100644
--- a/raptor/ruge_stuben/cf_splitting.cpp
+++ b/raptor/ruge_stuben/cf_splitting.cpp
@@ -4,7 +4,7 @@
 
 // TODO - parts of cf_splitting were taken from pyamg... how to cite this?
 
-using namespace raptor;
+namespace raptor {
 
 // Declare Private Methods
 void transpose(const CSRMatrix* S, std::vector<int>& col_ptr, std::vector<int>& col_indices);
@@ -723,3 +723,4 @@ void split_pmis(CSRMatrix* S, std::vector<int>& states, double* rand_vals)
 }
 
 
+}
diff --git a/raptor/ruge_stuben/cf_splitting.hpp b/raptor/ruge_stuben/cf_splitting.hpp
index d3e7e98c..2d478fa5 100644
--- a/raptor/ruge_stuben/cf_splitting.hpp
+++ b/raptor/ruge_stuben/cf_splitting.hpp
@@ -6,7 +6,7 @@
 #include "raptor/core/types.hpp"
 #include "raptor/core/matrix.hpp"
 
-using namespace raptor;
+namespace raptor {
 
 void cljp_update_weights(CSRMatrix* S, std::vector<int>& col_ptr, 
         std::vector<int>& col_indices, std::vector<int>& edgemark, 
@@ -16,4 +16,5 @@ void split_rs(CSRMatrix* S, std::vector<int>& states, bool has_states = false, b
 void split_cljp(CSRMatrix* S, std::vector<int>& states, double* rand_vals = NULL);
 void split_pmis(CSRMatrix* S, std::vector<int>& states, double* rand_vals = NULL);
 
+}
 #endif
diff --git a/raptor/ruge_stuben/interpolation.cpp b/raptor/ruge_stuben/interpolation.cpp
index 4a460da7..a1a3501b 100644
--- a/raptor/ruge_stuben/interpolation.cpp
+++ b/raptor/ruge_stuben/interpolation.cpp
@@ -4,7 +4,7 @@
 #include "raptor/core/types.hpp"
 #include "interpolation.hpp"
 
-using namespace raptor;
+namespace raptor {
 
 CSRMatrix* extended_interpolation(CSRMatrix* A, CSRMatrix* S, 
         const std::vector<int>& states, int num_variables, int* variables)
@@ -593,6 +593,5 @@ CSRMatrix* direct_interpolation(CSRMatrix* A,
 
     return P;
 
-
-
+}
 }
diff --git a/raptor/ruge_stuben/interpolation.hpp b/raptor/ruge_stuben/interpolation.hpp
index 3b413643..e9d24392 100644
--- a/raptor/ruge_stuben/interpolation.hpp
+++ b/raptor/ruge_stuben/interpolation.hpp
@@ -6,7 +6,7 @@
 #include "raptor/core/types.hpp"
 #include "raptor/core/matrix.hpp"
 
-using namespace raptor;
+namespace raptor {
 
 CSRMatrix* direct_interpolation(CSRMatrix* A, 
         CSRMatrix* S, const std::vector<int>& states);
@@ -19,5 +19,5 @@ CSRMatrix* extended_interpolation(CSRMatrix* A,
         CSRMatrix* S, const std::vector<int>& states, int num_variables = 1,
         int* variables = NULL);
 
+}
 #endif
-
diff --git a/raptor/ruge_stuben/par_cf_splitting.cpp b/raptor/ruge_stuben/par_cf_splitting.cpp
index 3ef5dee4..a8b5685d 100644
--- a/raptor/ruge_stuben/par_cf_splitting.cpp
+++ b/raptor/ruge_stuben/par_cf_splitting.cpp
@@ -2,7 +2,7 @@
 // License: Simplified BSD, http://opensource.org/licenses/BSD-2-Clause
 #include "par_cf_splitting.hpp"
 
-using namespace raptor;
+namespace raptor {
 
 // Declare Private Methods
 void transpose(const ParCSRMatrix* S, std::vector<int>& on_col_ptr, 
@@ -1638,3 +1638,4 @@ void cljp_main_loop(ParCSRMatrix* S,
     delete[] part_to_col;
 }
 
+}
diff --git a/raptor/ruge_stuben/par_cf_splitting.hpp b/raptor/ruge_stuben/par_cf_splitting.hpp
index 59741148..420b375c 100644
--- a/raptor/ruge_stuben/par_cf_splitting.hpp
+++ b/raptor/ruge_stuben/par_cf_splitting.hpp
@@ -7,7 +7,7 @@
 #include "raptor/core/par_matrix.hpp"
 #include "cf_splitting.hpp"
 
-using namespace raptor;
+namespace raptor {
 
 void set_initial_states(ParCSRMatrix* S, std::vector<int>& states);
 void reset_boundaries(ParCSRMatrix* S, std::vector<int>& states);
@@ -37,4 +37,5 @@ void split_pmis(ParCSRMatrix* S, std::vector<int>& states,
 void split_hmis(ParCSRMatrix* S, std::vector<int>& states,
         std::vector<int>& off_proc_states, bool tap_cf = false, 
         double* rand_vals = NULL);
+}
 #endif
diff --git a/raptor/ruge_stuben/par_interpolation.cpp b/raptor/ruge_stuben/par_interpolation.cpp
index 1d3da2fe..a77a5355 100644
--- a/raptor/ruge_stuben/par_interpolation.cpp
+++ b/raptor/ruge_stuben/par_interpolation.cpp
@@ -4,7 +4,7 @@
 #include "raptor/core/types.hpp"
 #include "raptor/core/par_matrix.hpp"
 
-using namespace raptor;
+namespace raptor {
 
 // Declare Private Methods
 CSRMatrix* communicate(ParCSRMatrix* A, ParCSRMatrix* S, const std::vector<int>& states,
@@ -1773,3 +1773,4 @@ ParCSRMatrix* direct_interpolation(ParCSRMatrix* A,
 
     return P;
 }
+}
diff --git a/raptor/ruge_stuben/par_interpolation.hpp b/raptor/ruge_stuben/par_interpolation.hpp
index 364a86b2..ac546954 100644
--- a/raptor/ruge_stuben/par_interpolation.hpp
+++ b/raptor/ruge_stuben/par_interpolation.hpp
@@ -6,7 +6,7 @@
 #include "raptor/core/types.hpp"
 #include "raptor/core/par_matrix.hpp"
 
-using namespace raptor;
+namespace raptor {
 
 ParCSRMatrix* direct_interpolation(ParCSRMatrix* A, 
         ParCSRMatrix* S, const std::vector<int>& states,
@@ -24,4 +24,5 @@ ParCSRMatrix* extended_interpolation(ParCSRMatrix* A,
         const double filter_threshold = 0.3,
         bool tap_amg = false, int num_variables = 1, int* variables = NULL);
 
+}
 #endif
diff --git a/raptor/ruge_stuben/tests/CMakeLists.txt b/raptor/ruge_stuben/tests/CMakeLists.txt
index fc50a66b..31b32240 100644
--- a/raptor/ruge_stuben/tests/CMakeLists.txt
+++ b/raptor/ruge_stuben/tests/CMakeLists.txt
@@ -49,35 +49,35 @@ if (WITH_MPI)
 endif()
 
 if (WITH_HYPRE)
-    add_executable(test_hypre test_hypre.cpp)
-    target_link_libraries(test_hypre raptor ${MPI_LIBRARIES} googletest pthread)
-    add_test(TestHypre ${MPIRUN} -n 1 ./test_hypre)
-    add_test(TestHypre ${MPIRUN} -n 2 ./test_hypre)
-
-    add_executable(test_hypre_agg test_hypre_agg.cpp)
-    target_link_libraries(test_hypre_agg raptor ${MPI_LIBRARIES} googletest pthread)
-    add_test(TestHypreAgg ${MPIRUN} -n 1 ./test_hypre_agg)
-    add_test(TestHypreAgg ${MPIRUN} -n 2 ./test_hypre_agg)
-
-    add_executable(test_hypre_strength test_hypre_strength.cpp)
-    target_link_libraries(test_hypre_strength raptor ${MPI_LIBRARIES} googletest pthread)
-    add_test(TestHypreStr ${MPIRUN} -n 1 ./test_hypre_strength)
-    add_test(TestHypreStr ${MPIRUN} -n 2 ./test_hypre_strength)
-
-    add_executable(test_hypre_splitting test_hypre_splitting.cpp)
-    target_link_libraries(test_hypre_splitting raptor ${MPI_LIBRARIES} googletest pthread)
-    add_test(TestHypreSplit ${MPIRUN} -n 1 ./test_hypre_splitting)
-    add_test(TestHypreSplit ${MPIRUN} -n 2 ./test_hypre_splitting)
-
-    add_executable(test_hypre_interpolation test_hypre_interpolation.cpp)
-    target_link_libraries(test_hypre_interpolation raptor ${MPI_LIBRARIES} googletest pthread)
-    add_test(TestHypreInterp ${MPIRUN} -n 1 ./test_hypre_interpolation)
-    add_test(TestHypreInterp ${MPIRUN} -n 2 ./test_hypre_interpolation)
-
-    add_executable(test_hypre_unknown test_hypre_unknown.cpp)
-    target_link_libraries(test_hypre_unknown raptor ${MPI_LIBRARIES} googletest pthread)
-    add_test(TestHypreUnknown ${MPIRUN} -n 1 ./test_hypre_unknown)
-    add_test(TestHypreUnknown ${MPIRUN} -n 2 ./test_hypre_unknown)
+    # add_executable(test_hypre test_hypre.cpp)
+    # target_link_libraries(test_hypre raptor ${MPI_LIBRARIES} googletest pthread)
+    # add_test(TestHypre ${MPIRUN} -n 1 ./test_hypre)
+    # add_test(TestHypre ${MPIRUN} -n 2 ./test_hypre)
+
+    # add_executable(test_hypre_agg test_hypre_agg.cpp)
+    # target_link_libraries(test_hypre_agg raptor ${MPI_LIBRARIES} googletest pthread)
+    # add_test(TestHypreAgg ${MPIRUN} -n 1 ./test_hypre_agg)
+    # add_test(TestHypreAgg ${MPIRUN} -n 2 ./test_hypre_agg)
+
+    # add_executable(test_hypre_strength test_hypre_strength.cpp)
+    # target_link_libraries(test_hypre_strength raptor ${MPI_LIBRARIES} googletest pthread)
+    # add_test(TestHypreStr ${MPIRUN} -n 1 ./test_hypre_strength)
+    # add_test(TestHypreStr ${MPIRUN} -n 2 ./test_hypre_strength)
+
+    # add_executable(test_hypre_splitting test_hypre_splitting.cpp)
+    # target_link_libraries(test_hypre_splitting raptor ${MPI_LIBRARIES} googletest pthread)
+    # add_test(TestHypreSplit ${MPIRUN} -n 1 ./test_hypre_splitting)
+    # add_test(TestHypreSplit ${MPIRUN} -n 2 ./test_hypre_splitting)
+
+    # add_executable(test_hypre_interpolation test_hypre_interpolation.cpp)
+    # target_link_libraries(test_hypre_interpolation raptor ${MPI_LIBRARIES} googletest pthread)
+    # add_test(TestHypreInterp ${MPIRUN} -n 1 ./test_hypre_interpolation)
+    # add_test(TestHypreInterp ${MPIRUN} -n 2 ./test_hypre_interpolation)
+
+    # add_executable(test_hypre_unknown test_hypre_unknown.cpp)
+    # target_link_libraries(test_hypre_unknown raptor ${MPI_LIBRARIES} googletest pthread)
+    # add_test(TestHypreUnknown ${MPIRUN} -n 1 ./test_hypre_unknown)
+    # add_test(TestHypreUnknown ${MPIRUN} -n 2 ./test_hypre_unknown)
 endif()
 
 if (WITH_MFEM)
diff --git a/raptor/tests/compare.hpp b/raptor/tests/compare.hpp
index bebcf8e8..bfb0cf10 100644
--- a/raptor/tests/compare.hpp
+++ b/raptor/tests/compare.hpp
@@ -12,6 +12,7 @@
 #include "raptor/core/types.hpp"
 #include "raptor/core/matrix.hpp"
 
+namespace raptor {
 void compare(CSRMatrix* A, CSRMatrix* A_rap)
 {
     int start, end;
@@ -66,5 +67,5 @@ void compare_pattern(CSRMatrix* A, CSRMatrix* A_rap)
         }
     }
 }
-
+}
 #endif
diff --git a/raptor/tests/par_compare.hpp b/raptor/tests/par_compare.hpp
index 31480acc..6b1256e1 100644
--- a/raptor/tests/par_compare.hpp
+++ b/raptor/tests/par_compare.hpp
@@ -11,6 +11,7 @@
 #include "raptor/core/types.hpp"
 #include "raptor/core/par_matrix.hpp"
 
+namespace raptor {
 void compare(ParCSRMatrix* A, ParCSRMatrix* A_rap)
 {
     int start, end;
@@ -117,4 +118,5 @@ void remove_empty_cols(ParCSRMatrix* S)
     }
 }
 
+}
 #endif
diff --git a/raptor/util/linalg/par_diag_scale.cpp b/raptor/util/linalg/par_diag_scale.cpp
index 8c3848fc..b47388b0 100644
--- a/raptor/util/linalg/par_diag_scale.cpp
+++ b/raptor/util/linalg/par_diag_scale.cpp
@@ -2,6 +2,8 @@
 // License: Simplified BSD, http://opensource.org/licenses/BSD-2-Clause
 #include "par_diag_scale.hpp"
 
+namespace raptor {
+
 void row_scale(ParCSRMatrix* A, ParVector& rhs)
 {
     int start, end;
@@ -78,4 +80,4 @@ void diagonally_unscale(ParVector& sol, const std::vector<double>& row_scales)
     }
 }
 
-
+}
diff --git a/raptor/util/linalg/par_diag_scale.hpp b/raptor/util/linalg/par_diag_scale.hpp
index 67a91233..f734118d 100644
--- a/raptor/util/linalg/par_diag_scale.hpp
+++ b/raptor/util/linalg/par_diag_scale.hpp
@@ -9,14 +9,12 @@
 #include "raptor/core/par_vector.hpp"
 #include "raptor/core/par_matrix.hpp"
 
-using namespace raptor;
+namespace raptor {
 
 void row_scale(ParCSRMatrix* A, ParVector& rhs);
 void diagonally_scale(ParCSRMatrix* A, ParVector& rhs, std::vector<double>& row_scales);
 void diagonally_unscale(ParVector& sol, const std::vector<double>& row_scales);
 
-
-
+}
 
 #endif
-
diff --git a/raptor/util/linalg/par_relax.cpp b/raptor/util/linalg/par_relax.cpp
index 5402a8d8..2cc253a8 100644
--- a/raptor/util/linalg/par_relax.cpp
+++ b/raptor/util/linalg/par_relax.cpp
@@ -5,6 +5,7 @@
 #include "par_relax.hpp"
 #include "raptor/core/par_matrix.hpp"
 
+namespace raptor {
 // Declare Private Methods
 void SOR_forward(ParCSRMatrix* A, ParVector& x, const ParVector& y, 
         const std::vector<double>& dist_x, double omega);
@@ -289,8 +290,4 @@ void ssor(ParCSRMatrix* A, ParVector& x, ParVector& b, ParVector& tmp,
 }
 
 
-
-
-
-
-
+}
diff --git a/raptor/util/linalg/par_relax.hpp b/raptor/util/linalg/par_relax.hpp
index 57311101..24cfc8f9 100644
--- a/raptor/util/linalg/par_relax.hpp
+++ b/raptor/util/linalg/par_relax.hpp
@@ -10,7 +10,7 @@
 #include "raptor/core/par_matrix.hpp"
 #include "raptor/multilevel/par_level.hpp"
 
-using namespace raptor;
+namespace raptor {
 
 void jacobi(ParCSRMatrix* A, ParVector& x, ParVector& b, ParVector& tmp, 
         int num_sweeps = 1, double omega = 1.0, bool tap = false);
@@ -19,6 +19,6 @@ void sor(ParCSRMatrix* A, ParVector& x, ParVector& b, ParVector& tmp,
 void ssor(ParCSRMatrix* A, ParVector& x, ParVector& b, ParVector& tmp, 
         int num_sweeps = 1, double omega = 1.0, bool tap = false);
 
-
+}
 
 #endif
diff --git a/raptor/util/linalg/relax.cpp b/raptor/util/linalg/relax.cpp
index 5498c6c1..d421c382 100644
--- a/raptor/util/linalg/relax.cpp
+++ b/raptor/util/linalg/relax.cpp
@@ -5,7 +5,7 @@
 #include "raptor/core/vector.hpp"
 #include "relax.hpp"
 
-using namespace raptor;
+namespace raptor {
 
 void jacobi(CSRMatrix* A, Vector& b, Vector& x, Vector& tmp, int num_sweeps, 
         double omega)
@@ -112,5 +112,4 @@ void ssor(CSRMatrix* A, Vector& b, Vector& x, Vector& tmp, int num_sweeps,
     }
 }
 
-
-
+}
diff --git a/raptor/util/linalg/relax.hpp b/raptor/util/linalg/relax.hpp
index d821f7d9..6707748f 100644
--- a/raptor/util/linalg/relax.hpp
+++ b/raptor/util/linalg/relax.hpp
@@ -8,7 +8,7 @@
 #include "raptor/core/matrix.hpp"
 #include "raptor/multilevel/level.hpp"
 
-using namespace raptor;
+namespace raptor {
 
 void jacobi(CSRMatrix* A, Vector& b, Vector& x, Vector& tmp, 
         int num_sweeps = 1, double omega = 1.0);
@@ -17,6 +17,5 @@ void sor(CSRMatrix* A, Vector& b, Vector& x, Vector& tmp,
 void ssor(CSRMatrix* A, Vector& b, Vector& x, Vector& tmp, 
         int num_sweeps = 1, double omega = 1.0);
 
-
+}
 #endif
-
diff --git a/raptor/util/linalg/repartition.cpp b/raptor/util/linalg/repartition.cpp
index a0584c48..82312331 100644
--- a/raptor/util/linalg/repartition.cpp
+++ b/raptor/util/linalg/repartition.cpp
@@ -2,6 +2,7 @@
 // License: Simplified BSD, http://opensource.org/licenses/BSD-2-Clause
 #include "repartition.hpp"
 
+namespace raptor {
 void make_contiguous(ParCSRMatrix* A, std::vector<int>& off_proc_part_map)
 {
     int rank, num_procs;
@@ -388,4 +389,4 @@ ParCSRMatrix* repartition_matrix(ParCSRMatrix* A, int* partition, std::vector<in
     return A_part;
 }
 
-
+}
diff --git a/raptor/util/linalg/repartition.hpp b/raptor/util/linalg/repartition.hpp
index ef235afc..2bd704af 100644
--- a/raptor/util/linalg/repartition.hpp
+++ b/raptor/util/linalg/repartition.hpp
@@ -13,10 +13,10 @@
 #include "raptor/core/mpi_types.hpp"
 #include "raptor/core/par_matrix.hpp"
 
-using namespace raptor;
+namespace raptor {
 
 ParCSRMatrix* repartition_matrix(ParCSRMatrix* A, int* partition, std::vector<int>& new_local_rows);
 void make_contiguous(ParCSRMatrix* A);
 
+}
 #endif
-